From 04bd4f6f4b84f39b8daf6c72a42371178c96aef1 Mon Sep 17 00:00:00 2001
From: Oliver Stolpe <oliver.stolpe@bih-charite.de>
Date: Mon, 25 Mar 2024 11:31:39 +0100
Subject: [PATCH] feat: add a flag for incidental findings (#1121) (#1466)

---
 .../components/CaseDetail/CardAnnotations.vue |  2 +
 .../src/components/CaseDetail/FlagIcon.vue    |  1 +
 clinvar_export/serializers.py                 |  1 +
 clinvar_export/tests/test_views_ajax.py       |  1 +
 .../tests/unit/data/firstUserAnnotation.json  |  4 +-
 .../management/commands/repair_result_set.py  |  1 +
 ..._structuralvariantflags_flag_incidental.py | 18 +++++++++
 svs/models/user_annos.py                      |  3 ++
 svs/serializers/user_annos.py                 |  1 +
 svs/tests/factories.py                        |  1 +
 svs/vueapp/src/stores/strucvarFlags/store.ts  |  1 +
 .../drf_spectacular/varfish_api_schema.yaml   | 12 ++++++
 varfish/vueapp/components.d.ts                |  7 ++++
 .../components/FlagsCard/FlagsCard.vue        |  3 ++
 .../varfish/components/FlagsCard/constants.ts |  6 +++
 variants/file_export.py                       |  1 +
 .../0071_smallvariantflags_flag_molecular.py  | 12 ------
 .../migrations/0102_auto_20240322_1502.py     | 37 +++++++++++++++++++
 variants/models/presets.py                    |  1 +
 variants/models/userannos.py                  |  3 ++
 variants/queries.py                           |  2 +
 variants/query_presets.py                     |  3 ++
 variants/query_schemas.py                     |  2 +
 variants/schemas/case-query-v1.json           | 11 ++++++
 ...ase-query-v1-01-minimal-with-defaults.json |  1 +
 ...e-query-v1-02-singleton-with-defaults.json |  1 +
 .../examples/case-query-v1-02-singleton.json  |  1 +
 variants/serializers/__init__.py              |  2 +
 variants/tests/data/query_settings.py         |  4 +-
 variants/tests/factories.py                   |  3 ++
 variants/tests/test_file_export.py            |  8 ++--
 variants/tests/test_models_presets.py         |  1 +
 variants/tests/test_query_presets.py          |  4 ++
 variants/tests/test_views_api.py              |  1 +
 .../components/FilterForm/FlagsPane.fields.js |  4 ++
 .../src/components/FilterForm/FlagsPane.vue   |  1 +
 variants/vueapp/src/stores/variantFlags.ts    |  1 +
 .../vueapp/tests/data/filter-query-store.json |  4 +-
 .../tests/data/listPresetSetResponse.json     |  4 +-
 .../tests/data/listQueryResultRowResult.json  |  4 +-
 .../tests/data/query-settings-singleton.json  |  4 +-
 .../tests/data/query-settings-trio.json       |  4 +-
 .../data/retrieveFlagsEtcPresetsResponse.json |  4 +-
 .../tests/data/retrievePresetSetResponse.json |  4 +-
 .../var-brca1-missense-benign-smallvar.json   |  4 +-
 .../data/var-mtdna-noncoding-smallvar.json    |  4 +-
 variants/vueapp/tests/data/variants-trio.json |  4 +-
 .../components/FilterForm/FlagsPane.spec.js   |  7 +++-
 48 files changed, 172 insertions(+), 41 deletions(-)
 create mode 100644 svs/migrations/0025_structuralvariantflags_flag_incidental.py
 create mode 100644 variants/migrations/0102_auto_20240322_1502.py

diff --git a/cases/vueapp/src/components/CaseDetail/CardAnnotations.vue b/cases/vueapp/src/components/CaseDetail/CardAnnotations.vue
index 7d12d488d..7432888d5 100644
--- a/cases/vueapp/src/components/CaseDetail/CardAnnotations.vue
+++ b/cases/vueapp/src/components/CaseDetail/CardAnnotations.vue
@@ -19,6 +19,7 @@ const svCommentsStore = useVariantCommentsStore()
 
 const flagIds = [
   'flag_bookmarked',
+  'flag_incidental',
   'flag_candidate',
   'flag_final_causative',
   'flag_for_validation',
@@ -42,6 +43,7 @@ const buildComputedAnnoCountByFlag = (theList: Map<string, any>) => {
   return computed<{ [flagId in FlagIds]: number }>(() => {
     const result = {
       flag_bookmarked: 0,
+      flag_incidental: 0,
       flag_candidate: 0,
       flag_final_causative: 0,
       flag_for_validation: 0,
diff --git a/cases/vueapp/src/components/CaseDetail/FlagIcon.vue b/cases/vueapp/src/components/CaseDetail/FlagIcon.vue
index a19fc4621..61b0254f6 100644
--- a/cases/vueapp/src/components/CaseDetail/FlagIcon.vue
+++ b/cases/vueapp/src/components/CaseDetail/FlagIcon.vue
@@ -9,6 +9,7 @@ const props = defineProps<{
 <template>
   <span>
     <i-fa-solid-star v-if="flag === 'flag_bookmarked'" />
+    <i-mdi-dice-5 v-else-if="flag === 'flag_incidental'" />
     <i-fa-solid-flask v-else-if="flag === 'flag_for_validation'" />
     <i-fa-solid-heart v-else-if="flag === 'flag_candidate'" />
     <i-fa-solid-flag-checkered v-else-if="flag === 'flag_final_causative'" />
diff --git a/clinvar_export/serializers.py b/clinvar_export/serializers.py
index ae0db2514..cde0ee2b8 100644
--- a/clinvar_export/serializers.py
+++ b/clinvar_export/serializers.py
@@ -415,6 +415,7 @@ class Meta:
                 "flag_molecular",
                 "flag_validation",
                 "flag_phenotype_match",
+                "flag_incidental",
                 "flag_summary",
             ]
         )
diff --git a/clinvar_export/tests/test_views_ajax.py b/clinvar_export/tests/test_views_ajax.py
index ebbbd0041..b2862ccf2 100644
--- a/clinvar_export/tests/test_views_ajax.py
+++ b/clinvar_export/tests/test_views_ajax.py
@@ -992,6 +992,7 @@ def test_query(self):
                         "flag_doesnt_segregate": False,
                         "flag_final_causative": False,
                         "flag_for_validation": False,
+                        "flag_incidental": False,
                         "flag_molecular": "",
                         "flag_no_disease_association": False,
                         "flag_phenotype_match": "",
diff --git a/clinvar_export/vueapp/tests/unit/data/firstUserAnnotation.json b/clinvar_export/vueapp/tests/unit/data/firstUserAnnotation.json
index b445dc3ba..5a5b83186 100644
--- a/clinvar_export/vueapp/tests/unit/data/firstUserAnnotation.json
+++ b/clinvar_export/vueapp/tests/unit/data/firstUserAnnotation.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:2f666481ce2a04bfee653e47261d9e7e611cba5d5788bc4156b8ff6070618f5e
-size 3109
+oid sha256:2ef3c2771c0dacedb593e42c9c7a92f67d24541d8d18201302a804f66f1fedad
+size 3141
diff --git a/maintenance/management/commands/repair_result_set.py b/maintenance/management/commands/repair_result_set.py
index 9f6aa3f17..cc81d380b 100644
--- a/maintenance/management/commands/repair_result_set.py
+++ b/maintenance/management/commands/repair_result_set.py
@@ -185,6 +185,7 @@ def _handle_case(self, case):  # noqa: C901
                     "flag_bookmarked",
                     "flag_segregates",
                     "flag_validation",
+                    "flag_incidental",
                     "flag_for_validation",
                     "flag_final_causative",
                     "flag_phenotype_match",
diff --git a/svs/migrations/0025_structuralvariantflags_flag_incidental.py b/svs/migrations/0025_structuralvariantflags_flag_incidental.py
new file mode 100644
index 000000000..60d5048bd
--- /dev/null
+++ b/svs/migrations/0025_structuralvariantflags_flag_incidental.py
@@ -0,0 +1,18 @@
+# Generated by Django 3.2.24 on 2024-03-22 15:02
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("svs", "0024_clear_sv_queries"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="structuralvariantflags",
+            name="flag_incidental",
+            field=models.BooleanField(default=False),
+        ),
+    ]
diff --git a/svs/models/user_annos.py b/svs/models/user_annos.py
index 085ca0d33..a1d31ccf2 100644
--- a/svs/models/user_annos.py
+++ b/svs/models/user_annos.py
@@ -116,6 +116,8 @@ class StructuralVariantFlags(HumanReadableMixin, _UserAnnotation):
     flag_segregates = models.BooleanField(default=False, null=False)
     #: Variant does not segregate
     flag_doesnt_segregate = models.BooleanField(default=False, null=False)
+    #: Variant is an incidental finding
+    flag_incidental = models.BooleanField(default=False, null=False)
 
     # Choice fields for gradual rating
 
@@ -155,6 +157,7 @@ def no_flags_set(self):
                 self.flag_no_disease_association,
                 self.flag_segregates,
                 self.flag_doesnt_segregate,
+                self.flag_incidental,
                 self.flag_molecular != "empty",
                 self.flag_visual != "empty",
                 self.flag_validation != "empty",
diff --git a/svs/serializers/user_annos.py b/svs/serializers/user_annos.py
index 71b772427..18162de68 100644
--- a/svs/serializers/user_annos.py
+++ b/svs/serializers/user_annos.py
@@ -90,6 +90,7 @@ class Meta:
             "flag_molecular",
             "flag_validation",
             "flag_phenotype_match",
+            "flag_incidental",
             "flag_summary",
         )
         read_only_fields = ("sodar_uuid", "date_created", "date_modified", "case")
diff --git a/svs/tests/factories.py b/svs/tests/factories.py
index d49060834..7eae87412 100644
--- a/svs/tests/factories.py
+++ b/svs/tests/factories.py
@@ -247,6 +247,7 @@ class Meta:
     flag_no_disease_association = False
     flag_segregates = False
     flag_doesnt_segregate = False
+    flag_incidental = False
 
     flag_molecular = "empty"
     flag_visual = "empty"
diff --git a/svs/vueapp/src/stores/strucvarFlags/store.ts b/svs/vueapp/src/stores/strucvarFlags/store.ts
index ce1a618d7..6498361a0 100644
--- a/svs/vueapp/src/stores/strucvarFlags/store.ts
+++ b/svs/vueapp/src/stores/strucvarFlags/store.ts
@@ -18,6 +18,7 @@ type StructuralVariantFlags = any
 
 export const emptyFlagsTemplate = Object.freeze({
   flag_bookmarked: false,
+  flag_incidental: false,
   flag_for_validation: false,
   flag_candidate: false,
   flag_final_causative: false,
diff --git a/varfish/tests/drf_spectacular/varfish_api_schema.yaml b/varfish/tests/drf_spectacular/varfish_api_schema.yaml
index cff4c85af..6067792a8 100644
--- a/varfish/tests/drf_spectacular/varfish_api_schema.yaml
+++ b/varfish/tests/drf_spectacular/varfish_api_schema.yaml
@@ -10872,6 +10872,8 @@ components:
           type: boolean
         flag_bookmarked:
           type: boolean
+        flag_incidental:
+          type: boolean
         flag_candidate:
           type: boolean
         flag_doesnt_segregate:
@@ -12711,6 +12713,8 @@ components:
           type: boolean
         flag_bookmarked:
           type: boolean
+        flag_incidental:
+          type: boolean
         flag_candidate:
           type: boolean
         flag_doesnt_segregate:
@@ -13287,6 +13291,8 @@ components:
           maxLength: 512
         flag_bookmarked:
           type: boolean
+        flag_incidental:
+          type: boolean
         flag_candidate:
           type: boolean
         flag_final_causative:
@@ -13476,6 +13482,8 @@ components:
           $ref: '#/components/schemas/VariantRatingEnum'
         flag_phenotype_match:
           $ref: '#/components/schemas/VariantRatingEnum'
+        flag_incidental:
+          type: boolean
         flag_summary:
           $ref: '#/components/schemas/VariantRatingEnum'
     PatchedTargetBedFile:
@@ -14361,6 +14369,8 @@ components:
           maxLength: 512
         flag_bookmarked:
           type: boolean
+        flag_incidental:
+          type: boolean
         flag_candidate:
           type: boolean
         flag_final_causative:
@@ -14940,6 +14950,8 @@ components:
           $ref: '#/components/schemas/VariantRatingEnum'
         flag_phenotype_match:
           $ref: '#/components/schemas/VariantRatingEnum'
+        flag_incidental:
+          type: boolean
         flag_summary:
           $ref: '#/components/schemas/VariantRatingEnum'
       required:
diff --git a/varfish/vueapp/components.d.ts b/varfish/vueapp/components.d.ts
index 9e62c632e..c6eb8729b 100644
--- a/varfish/vueapp/components.d.ts
+++ b/varfish/vueapp/components.d.ts
@@ -25,6 +25,9 @@ declare module 'vue' {
     IFaSolidCode: typeof import('~icons/fa-solid/code')['default']
     IFaSolidComment: typeof import('~icons/fa-solid/comment')['default']
     IFaSolidDatabase: typeof import('~icons/fa-solid/database')['default']
+    IFaSolidDice: typeof import('~icons/fa-solid/dice')['default']
+    IFaSolidDice5Outline: typeof import('~icons/fa-solid/dice5-outline')['default']
+    IFaSolidDiceFive: typeof import('~icons/fa-solid/dice-five')['default']
     IFaSolidExclamationCircle: typeof import('~icons/fa-solid/exclamation-circle')['default']
     IFaSolidFlagCheckered: typeof import('~icons/fa-solid/flag-checkered')['default']
     IFaSolidFlask: typeof import('~icons/fa-solid/flask')['default']
@@ -71,6 +74,8 @@ declare module 'vue' {
     IMdiContentCopy: typeof import('~icons/mdi/content-copy')['default']
     IMdiDelete: typeof import('~icons/mdi/delete')['default']
     IMdiDeleteForever: typeof import('~icons/mdi/delete-forever')['default']
+    IMdiDice5: typeof import('~icons/mdi/dice5')['default']
+    IMdiDice5Outline: typeof import('~icons/mdi/dice5-outline')['default']
     IMdiDoNotDisturbOn: typeof import('~icons/mdi/do-not-disturb-on')['default']
     IMdiDotsHorizontal: typeof import('~icons/mdi/dots-horizontal')['default']
     IMdiDownload: typeof import('~icons/mdi/download')['default']
@@ -99,6 +104,8 @@ declare module 'vue' {
     IMdiPodium: typeof import('~icons/mdi/podium')['default']
     IMdiRefresh: typeof import('~icons/mdi/refresh')['default']
     IMdiSquareEditOutline: typeof import('~icons/mdi/square-edit-outline')['default']
+    IMdiTableColumnWidth: typeof import('~icons/mdi/table-column-width')['default']
+    IMdiTableMergeCells: typeof import('~icons/mdi/table-merge-cells')['default']
     IMdiToggleSwitchOutline: typeof import('~icons/mdi/toggle-switch-outline')['default']
     IMdiTools: typeof import('~icons/mdi/tools')['default']
     IMdiUndoVariant: typeof import('~icons/mdi/undo-variant')['default']
diff --git a/varfish/vueapp/src/varfish/components/FlagsCard/FlagsCard.vue b/varfish/vueapp/src/varfish/components/FlagsCard/FlagsCard.vue
index 52b438862..b9d1c37f7 100644
--- a/varfish/vueapp/src/varfish/components/FlagsCard/FlagsCard.vue
+++ b/varfish/vueapp/src/varfish/components/FlagsCard/FlagsCard.vue
@@ -28,6 +28,8 @@ const flagsSubmitted = computed(() => {
   return (
     flagsToSubmit.value.flag_bookmarked ===
       props.flagsStore.flags.flag_bookmarked &&
+    flagsToSubmit.value.flag_incidental ===
+      props.flagsStore.flags.flag_incidental &&
     flagsToSubmit.value.flag_for_validation ===
       props.flagsStore.flags.flag_for_validation &&
     flagsToSubmit.value.flag_candidate ===
@@ -54,6 +56,7 @@ const flagsSubmitted = computed(() => {
 const resetFlags = async () => {
   if (props.flagsStore.flags) {
     flagsToSubmit.value.flag_bookmarked = props.flagsStore.flags.flag_bookmarked
+    flagsToSubmit.value.flag_incidental = props.flagsStore.flags.flag_incidental
     flagsToSubmit.value.flag_for_validation =
       props.flagsStore.flags.flag_for_validation
     flagsToSubmit.value.flag_candidate = props.flagsStore.flags.flag_candidate
diff --git a/varfish/vueapp/src/varfish/components/FlagsCard/constants.ts b/varfish/vueapp/src/varfish/components/FlagsCard/constants.ts
index eb57c0477..02acdbc6c 100644
--- a/varfish/vueapp/src/varfish/components/FlagsCard/constants.ts
+++ b/varfish/vueapp/src/varfish/components/FlagsCard/constants.ts
@@ -4,6 +4,7 @@ export interface BooleanFlagSpec {
   icon: string
   key:
     | 'flag_bookmarked'
+    | 'flag_incidental'
     | 'flag_for_validation'
     | 'flag_candidate'
     | 'flag_final_causative'
@@ -24,6 +25,11 @@ export const BOOLEAN_FLAGS: BooleanFlagSpec[] = [
     icon: 'mdi-flask-empty',
     key: 'flag_for_validation',
   },
+  {
+    label: 'incidental finding',
+    icon: 'mdi-dice-5',
+    key: 'flag_incidental',
+  },
   {
     label: 'candidate',
     icon: 'mdi-cards-heart',
diff --git a/variants/file_export.py b/variants/file_export.py
index d5f584a53..8b9d43838 100644
--- a/variants/file_export.py
+++ b/variants/file_export.py
@@ -145,6 +145,7 @@ def to_str(val):
     ("flag_no_disease_association", "Flag: selected for no known disease association", str),
     ("flag_segregates", "Flag: selected as segregating variant", str),
     ("flag_doesnt_segregate", "Flag: selected as not segregating variant", str),
+    ("flag_incidental", "Flag: selected as incidental finding", str),
     ("flag_molecular", "Rating: variant is molecular", str),
     ("flag_visual", "Rating: visual inspection of alignment", str),
     ("flag_validation", "Rating: validation result", str),
diff --git a/variants/migrations/0071_smallvariantflags_flag_molecular.py b/variants/migrations/0071_smallvariantflags_flag_molecular.py
index fc50b5504..99bc1f0e8 100644
--- a/variants/migrations/0071_smallvariantflags_flag_molecular.py
+++ b/variants/migrations/0071_smallvariantflags_flag_molecular.py
@@ -4,16 +4,6 @@
 
 from django.db import migrations, models
 
-from variants.models import SmallVariantComment, SmallVariantFlags
-
-
-# Was in migration 0062 before. Didn't work anymore, because of the new field in SmallVariantFlags
-def update_chromosome_no_in_existing_flags_and_comments(apps, schema_editor):
-    if not schema_editor.connection.alias == "default":
-        return
-    for o in list(SmallVariantFlags.objects.all()) + list(SmallVariantComment.objects.all()):
-        o.save()
-
 
 class Migration(migrations.Migration):
     dependencies = [
@@ -35,6 +25,4 @@ class Migration(migrations.Migration):
                 max_length=32,
             ),
         ),
-        # Was in migration 0062 before. Didn't work anymore, because of the new field in SmallVariantFlags
-        migrations.RunPython(update_chromosome_no_in_existing_flags_and_comments),
     ]
diff --git a/variants/migrations/0102_auto_20240322_1502.py b/variants/migrations/0102_auto_20240322_1502.py
new file mode 100644
index 000000000..8b6069d5a
--- /dev/null
+++ b/variants/migrations/0102_auto_20240322_1502.py
@@ -0,0 +1,37 @@
+# Generated by Django 3.2.24 on 2024-03-22 15:02
+
+from django.db import migrations, models
+
+from variants.models import SmallVariantComment, SmallVariantFlags
+
+
+# Was in migration 0062 before. Didn't work anymore, because of the new field in SmallVariantFlags
+# Was in migration 0071 before
+def update_chromosome_no_in_existing_flags_and_comments(apps, schema_editor):
+    if not schema_editor.connection.alias == "default":
+        return
+    for o in list(SmallVariantFlags.objects.all()) + list(SmallVariantComment.objects.all()):
+        o.save()
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("variants", "0101_auto_20240301_1141_not_null_sodar_field"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="flagsetcpresets",
+            name="flag_incidental",
+            field=models.BooleanField(default=True),
+        ),
+        migrations.AddField(
+            model_name="smallvariantflags",
+            name="flag_incidental",
+            field=models.BooleanField(default=False),
+        ),
+        # Was in migration 0062 before. Didn't work anymore, because of the new field in SmallVariantFlags
+        # Was in migration 0071 before
+        migrations.RunPython(update_chromosome_no_in_existing_flags_and_comments),
+    ]
diff --git a/variants/models/presets.py b/variants/models/presets.py
index 6aa78f421..3f29023dd 100644
--- a/variants/models/presets.py
+++ b/variants/models/presets.py
@@ -235,6 +235,7 @@ class FlagsEtcPresets(PresetBase):
     clinvar_include_pathogenic = models.BooleanField(null=False, default=True)
     clinvar_include_uncertain_significance = models.BooleanField(null=False, default=True)
     flag_bookmarked = models.BooleanField(null=False, default=True)
+    flag_incidental = models.BooleanField(null=False, default=True)
     flag_candidate = models.BooleanField(null=False, default=True)
     flag_doesnt_segregate = models.BooleanField(null=False, default=True)
     flag_final_causative = models.BooleanField(null=False, default=True)
diff --git a/variants/models/userannos.py b/variants/models/userannos.py
index 5496f0d09..a1c0238f0 100644
--- a/variants/models/userannos.py
+++ b/variants/models/userannos.py
@@ -211,6 +211,8 @@ class SmallVariantFlags(GetGeneSymbolsMixin, HumanReadableMixin, models.Model):
 
     #: Bookmarked: saved for later
     flag_bookmarked = models.BooleanField(default=False, null=False)
+    #: Incidental finding
+    flag_incidental = models.BooleanField(default=False, null=False)
     #: Candidate variant
     flag_candidate = models.BooleanField(default=False, null=False)
     #: Finally selected causative variant
@@ -261,6 +263,7 @@ def no_flags_set(self):
         return not any(
             (
                 self.flag_bookmarked,
+                self.flag_incidental,
                 self.flag_candidate,
                 self.flag_final_causative,
                 self.flag_for_validation,
diff --git a/variants/queries.py b/variants/queries.py
index ff22d4c7d..55a35e4a9 100644
--- a/variants/queries.py
+++ b/variants/queries.py
@@ -1210,6 +1210,7 @@ def __init__(self, *args, **kwargs):
                 [
                     func.count(SmallVariantFlags.sa.id).label("flag_count"),
                     func.bool_or(SmallVariantFlags.sa.flag_bookmarked).label("flag_bookmarked"),
+                    func.bool_or(SmallVariantFlags.sa.flag_incidental).label("flag_incidental"),
                     func.bool_or(SmallVariantFlags.sa.flag_candidate).label("flag_candidate"),
                     func.bool_or(SmallVariantFlags.sa.flag_segregates).label("flag_segregates"),
                     func.bool_or(SmallVariantFlags.sa.flag_doesnt_segregate).label(
@@ -1256,6 +1257,7 @@ def extend_fields(self, _query_parts):
         return [
             self.subquery.c.flag_count,
             self.subquery.c.flag_bookmarked,
+            self.subquery.c.flag_incidental,
             self.subquery.c.flag_candidate,
             self.subquery.c.flag_segregates,
             self.subquery.c.flag_doesnt_segregate,
diff --git a/variants/query_presets.py b/variants/query_presets.py
index 2fa0d4c71..e5a6085d2 100644
--- a/variants/query_presets.py
+++ b/variants/query_presets.py
@@ -914,6 +914,7 @@ class _FlagsEtcPresets:
         "clinvar_include_pathogenic": True,
         "clinvar_include_uncertain_significance": False,
         "flag_bookmarked": True,
+        "flag_incidental": True,
         "flag_candidate": True,
         "flag_doesnt_segregate": True,
         "flag_final_causative": True,
@@ -949,6 +950,7 @@ class _FlagsEtcPresets:
     #: Presets for the "Clinvar only" flags etc. settings
     clinvar_only: typing.Dict[str, typing.Any] = {
         "flag_bookmarked": True,
+        "flag_incidental": True,
         "flag_candidate": True,
         "flag_doesnt_segregate": True,
         "flag_final_causative": True,
@@ -989,6 +991,7 @@ class _FlagsEtcPresets:
         "clinvar_include_pathogenic": True,
         "clinvar_include_uncertain_significance": False,
         "flag_bookmarked": True,
+        "flag_incidental": True,
         "flag_candidate": True,
         "flag_doesnt_segregate": True,
         "flag_final_causative": True,
diff --git a/variants/query_schemas.py b/variants/query_schemas.py
index 10dfc2744..30c5ef063 100644
--- a/variants/query_schemas.py
+++ b/variants/query_schemas.py
@@ -200,6 +200,7 @@ class CaseQueryV1:
 
     flag_simple_empty: bool = True
     flag_bookmarked: bool = True
+    flag_incidental: bool = True
     flag_candidate: bool = True
     flag_doesnt_segregate: bool = True
     flag_final_causative: bool = True
@@ -343,6 +344,7 @@ def convert(self, case: Case, query: CaseQueryV1) -> typing.Dict[str, typing.Any
             "clinvar_include_pathogenic": query.clinvar_include_pathogenic,
             "flag_simple_empty": query.flag_simple_empty,
             "flag_bookmarked": query.flag_bookmarked,
+            "flag_incidental": query.flag_incidental,
             "flag_candidate": query.flag_candidate,
             "flag_doesnt_segregate": query.flag_doesnt_segregate,
             "flag_final_causative": query.flag_final_causative,
diff --git a/variants/schemas/case-query-v1.json b/variants/schemas/case-query-v1.json
index c752aab37..858fb38ed 100644
--- a/variants/schemas/case-query-v1.json
+++ b/variants/schemas/case-query-v1.json
@@ -743,6 +743,17 @@
         false
       ]
     },
+    "flag_incidental": {
+      "$id": "#/properties/flag_incidental",
+      "type": "boolean",
+      "title": "Include variants marked with \"incidental\" flag",
+      "description": "When set (default) then variants that have the \"incidental\" simple flag set are included in the result",
+      "default": true,
+      "examples": [
+        true,
+        false
+      ]
+    },
     "flag_candidate": {
       "$id": "#/properties/flag_candidate",
       "type": "boolean",
diff --git a/variants/schemas/examples/case-query-v1-01-minimal-with-defaults.json b/variants/schemas/examples/case-query-v1-01-minimal-with-defaults.json
index 6eaedcef6..855d11a3c 100644
--- a/variants/schemas/examples/case-query-v1-01-minimal-with-defaults.json
+++ b/variants/schemas/examples/case-query-v1-01-minimal-with-defaults.json
@@ -31,6 +31,7 @@
   "var_type_mnv": true,
   "flag_simple_empty": true,
   "flag_bookmarked": true,
+  "flag_incidental": true,
   "flag_candidate": true,
   "flag_doesnt_segregate": true,
   "flag_final_causative": true,
diff --git a/variants/schemas/examples/case-query-v1-02-singleton-with-defaults.json b/variants/schemas/examples/case-query-v1-02-singleton-with-defaults.json
index 7768e64d3..10364301d 100644
--- a/variants/schemas/examples/case-query-v1-02-singleton-with-defaults.json
+++ b/variants/schemas/examples/case-query-v1-02-singleton-with-defaults.json
@@ -38,6 +38,7 @@
   "exac_heterozygous": 60,
   "exac_homozygous": 0,
   "flag_bookmarked": true,
+  "flag_incidental": true,
   "flag_candidate": true,
   "flag_doesnt_segregate": true,
   "flag_final_causative": true,
diff --git a/variants/schemas/examples/case-query-v1-02-singleton.json b/variants/schemas/examples/case-query-v1-02-singleton.json
index 8dfc77e6e..86c058aa3 100644
--- a/variants/schemas/examples/case-query-v1-02-singleton.json
+++ b/variants/schemas/examples/case-query-v1-02-singleton.json
@@ -37,6 +37,7 @@
   "exac_heterozygous": 60,
   "exac_homozygous": 0,
   "flag_bookmarked": true,
+  "flag_incidental": true,
   "flag_candidate": true,
   "flag_doesnt_segregate": true,
   "flag_final_causative": true,
diff --git a/variants/serializers/__init__.py b/variants/serializers/__init__.py
index bc324f8f7..bdae1c874 100644
--- a/variants/serializers/__init__.py
+++ b/variants/serializers/__init__.py
@@ -283,6 +283,7 @@ class SmallVariantForExtendedResultSerializer(serializers.Serializer):
     # Joined fields (ExtendQueryPartsFlagsJoinAndFilter)
     flag_count = serializers.IntegerField()
     flag_bookmarked = serializers.BooleanField()
+    flag_incidental = serializers.BooleanField()
     flag_candidate = serializers.BooleanField()
     flag_segregates = serializers.BooleanField()
     flag_doesnt_segregate = serializers.BooleanField()
@@ -711,6 +712,7 @@ class Meta:
             "reference",
             "alternative",
             "flag_bookmarked",
+            "flag_incidental",
             "flag_candidate",
             "flag_final_causative",
             "flag_for_validation",
diff --git a/variants/tests/data/query_settings.py b/variants/tests/data/query_settings.py
index ffdb08fb9..2bde6b9f6 100644
--- a/variants/tests/data/query_settings.py
+++ b/variants/tests/data/query_settings.py
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:e9636110e1580cb0d4f67a1b5e6b8dc3dd5e85cbef2bde6355687eeff4e59f3d
-size 9483
+oid sha256:790929d1cbfa778c688bdd8885b5403751c6ce5baf4028add6307b91b3d94a53
+size 9541
diff --git a/variants/tests/factories.py b/variants/tests/factories.py
index e0b32ac86..3975d211a 100644
--- a/variants/tests/factories.py
+++ b/variants/tests/factories.py
@@ -193,6 +193,7 @@ class FormDataFactory(FormDataFactoryBase):
     genomic_region: str = ""
     gene_allowlist: str = ""
     flag_bookmarked: bool = True
+    flag_incidental: bool = True
     flag_candidate: bool = True
     flag_final_causative: bool = True
     flag_for_validation: bool = True
@@ -253,6 +254,7 @@ class ChromosomalPositionFormDataFactoryBase:
 @attr.s(auto_attribs=True)
 class FlagsFormDataFactoryBase:
     flag_bookmarked: bool = True
+    flag_incidental: bool = True
     flag_candidate: bool = False
     flag_final_causative: bool = False
     flag_for_validation: bool = False
@@ -943,6 +945,7 @@ class Meta:
     case = factory.SubFactory(CaseFactory)
     flag_bookmarked = True
     flag_candidate = False
+    flag_incidental = False
     flag_final_causative = False
     flag_for_validation = False
     flag_no_disease_association = False
diff --git a/variants/tests/test_file_export.py b/variants/tests/test_file_export.py
index 67c04f2ed..20342b62c 100644
--- a/variants/tests/test_file_export.py
+++ b/variants/tests/test_file_export.py
@@ -190,9 +190,9 @@ def _test_tabular(self, arrs, has_trailing, janno_enable, database):
         self.assertEquals(len(arrs), 4 + int(has_trailing))
         # TODO: also test without flags and comments
         if not janno_enable:
-            self.assertEquals(len(arrs[0]), 57)
-        else:
             self.assertEquals(len(arrs[0]), 58)
+        else:
+            self.assertEquals(len(arrs[0]), 59)
         self.assertSequenceEqual(arrs[0][:3], ["Chromosome", "Position", "Reference bases"])
         self.assertSequenceEqual(
             arrs[0][-5:],
@@ -376,7 +376,7 @@ def test_export_tsv(self):
     def _test_tabular(self, arrs, has_trailing):
         self.assertEquals(len(arrs), 5 + int(has_trailing))
         # TODO: also test without flags and comments
-        self.assertEquals(len(arrs[0]), 57)
+        self.assertEquals(len(arrs[0]), 58)
         self.assertSequenceEqual(arrs[0][:3], ["Sample", "Chromosome", "Position"])
         self.assertEqual(arrs[0][-1], "sample Alternate allele fraction")
         members = sorted(self.project.get_members())
@@ -594,7 +594,7 @@ def test_export_tsv_as_contributor_for_cohort_by_superuser(self):
     def _test_tabular(self, arrs, ref, has_trailing, smallvars):
         self.assertEquals(len(arrs), ref + int(has_trailing))
         # TODO: also test without flags and comments
-        self.assertEquals(len(arrs[0]), 57)
+        self.assertEquals(len(arrs[0]), 58)
         self.assertSequenceEqual(arrs[0][:3], ["Sample", "Chromosome", "Position"])
         self.assertEqual(arrs[0][-1], "sample Alternate allele fraction")
         for i, small_var in enumerate(sorted(smallvars, key=lambda x: (x.chromosome_no, x.start))):
diff --git a/variants/tests/test_models_presets.py b/variants/tests/test_models_presets.py
index c742eba48..fff7f3479 100644
--- a/variants/tests/test_models_presets.py
+++ b/variants/tests/test_models_presets.py
@@ -317,6 +317,7 @@ def test_create_as_copy_of_factory_preset(self):
             "clinvar_include_pathogenic": True,
             "clinvar_include_uncertain_significance": False,
             "flag_bookmarked": True,
+            "flag_incidental": True,
             "flag_candidate": True,
             "flag_doesnt_segregate": True,
             "flag_final_causative": True,
diff --git a/variants/tests/test_query_presets.py b/variants/tests/test_query_presets.py
index 41e1208aa..cba8ffd9d 100644
--- a/variants/tests/test_query_presets.py
+++ b/variants/tests/test_query_presets.py
@@ -1485,6 +1485,7 @@ def testToSettingsDefaults(self):
                 "clinvar_include_uncertain_significance": False,
                 "clinvar_paranoid_mode": False,
                 "flag_bookmarked": True,
+                "flag_incidental": True,
                 "flag_candidate": True,
                 "flag_doesnt_segregate": True,
                 "flag_final_causative": True,
@@ -1523,6 +1524,7 @@ def testToSettingsClinvarOnly(self):
             query_presets.FlagsEtc.CLINVAR_ONLY.to_settings(),
             {
                 "flag_bookmarked": True,
+                "flag_incidental": True,
                 "flag_candidate": True,
                 "flag_doesnt_segregate": True,
                 "flag_final_causative": True,
@@ -1567,6 +1569,7 @@ def testToSettingsUserFlagged(self):
                 "clinvar_include_pathogenic": True,
                 "clinvar_include_uncertain_significance": False,
                 "flag_bookmarked": True,
+                "flag_incidental": True,
                 "flag_candidate": True,
                 "flag_doesnt_segregate": True,
                 "flag_final_causative": True,
@@ -1747,6 +1750,7 @@ def testToSettingsDefaults(self):
                 "exac_heterozygous": 10,
                 "exac_homozygous": 0,
                 "flag_bookmarked": True,
+                "flag_incidental": True,
                 "flag_candidate": True,
                 "flag_doesnt_segregate": True,
                 "flag_final_causative": True,
diff --git a/variants/tests/test_views_api.py b/variants/tests/test_views_api.py
index 953f9a1a0..2cd2a68e1 100644
--- a/variants/tests/test_views_api.py
+++ b/variants/tests/test_views_api.py
@@ -705,6 +705,7 @@ def test_get_success(self):
                 "clinvar_include_pathogenic": True,
                 "clinvar_include_uncertain_significance": False,
                 "flag_bookmarked": True,
+                "flag_incidental": True,
                 "flag_candidate": True,
                 "flag_doesnt_segregate": True,
                 "flag_final_causative": True,
diff --git a/variants/vueapp/src/components/FilterForm/FlagsPane.fields.js b/variants/vueapp/src/components/FilterForm/FlagsPane.fields.js
index d73ad94c7..36c8630b7 100644
--- a/variants/vueapp/src/components/FilterForm/FlagsPane.fields.js
+++ b/variants/vueapp/src/components/FilterForm/FlagsPane.fields.js
@@ -3,6 +3,10 @@ export const simpleFlags = Object.freeze([
     id: 'flag_bookmarked',
     label: 'bookmarked',
   },
+  {
+    id: 'flag_incidental',
+    label: 'incidental finding',
+  },
   {
     id: 'flag_candidate',
     label: 'candidate',
diff --git a/variants/vueapp/src/components/FilterForm/FlagsPane.vue b/variants/vueapp/src/components/FilterForm/FlagsPane.vue
index fac2925a5..370d4db5b 100644
--- a/variants/vueapp/src/components/FilterForm/FlagsPane.vue
+++ b/variants/vueapp/src/components/FilterForm/FlagsPane.vue
@@ -57,6 +57,7 @@ const props = defineProps({
             <i-fa-solid-thumbs-down
               v-if="flag.id === 'flag_doesnt_segregate'"
             />
+            <i-mdi-dice-5 v-if="flag.id === 'flag_incidental'" />
             {{ flag.label }}
           </label>
         </div>
diff --git a/variants/vueapp/src/stores/variantFlags.ts b/variants/vueapp/src/stores/variantFlags.ts
index 5d492e038..992a650fc 100644
--- a/variants/vueapp/src/stores/variantFlags.ts
+++ b/variants/vueapp/src/stores/variantFlags.ts
@@ -46,6 +46,7 @@ export const useVariantFlagsStore = defineStore('variantFlags', () => {
   /** Template object to use for for empty flags. */
   const emptyFlagsTemplate = Object.freeze({
     flag_bookmarked: false,
+    flag_incidental: false,
     flag_for_validation: false,
     flag_candidate: false,
     flag_final_causative: false,
diff --git a/variants/vueapp/tests/data/filter-query-store.json b/variants/vueapp/tests/data/filter-query-store.json
index 3959c11bc..3104ebf87 100644
--- a/variants/vueapp/tests/data/filter-query-store.json
+++ b/variants/vueapp/tests/data/filter-query-store.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:9afa2fc5d2697f9fe78eb31ae85c18c24d66e8a833996069fa5b4186b8e3425f
-size 64955
+oid sha256:9c61a95d56b5b6cf2660532227ff897be24fdc4085890462e06211314ee348ee
+size 65108
diff --git a/variants/vueapp/tests/data/listPresetSetResponse.json b/variants/vueapp/tests/data/listPresetSetResponse.json
index f09efbae8..e7f7e27ea 100644
--- a/variants/vueapp/tests/data/listPresetSetResponse.json
+++ b/variants/vueapp/tests/data/listPresetSetResponse.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:733690ec41e984ece20bb71ebe133489f522437ff5e70652362bd31491cff15f
-size 5765
+oid sha256:bd7ba3da6684f89d491f66b1cfbf2c5c120cbfe1cf8d1e6565d4a59bd2a1afa1
+size 5798
diff --git a/variants/vueapp/tests/data/listQueryResultRowResult.json b/variants/vueapp/tests/data/listQueryResultRowResult.json
index 7627f6b82..927083fbd 100644
--- a/variants/vueapp/tests/data/listQueryResultRowResult.json
+++ b/variants/vueapp/tests/data/listQueryResultRowResult.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:292c064ca13dca852686b104e6aba305fdd3bbc9ba8606f85cca78aece562357
-size 12958
+oid sha256:bdc8caa43d9faef31fea151ca9cd38ebeb3210d40b6a25d64222e12701902f82
+size 13059
diff --git a/variants/vueapp/tests/data/query-settings-singleton.json b/variants/vueapp/tests/data/query-settings-singleton.json
index 8d1b2939e..e1db51276 100644
--- a/variants/vueapp/tests/data/query-settings-singleton.json
+++ b/variants/vueapp/tests/data/query-settings-singleton.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:c21edaf4edc1794f4bcb9132cd6255fbdf30cc17ebca415c92cc18913af65da6
-size 3628
+oid sha256:44aca3fb3c548c48e73d9485423222bd6fc4588c510f89ace433d361e425032c
+size 3655
diff --git a/variants/vueapp/tests/data/query-settings-trio.json b/variants/vueapp/tests/data/query-settings-trio.json
index 66d44f2a8..0b92f8f87 100644
--- a/variants/vueapp/tests/data/query-settings-trio.json
+++ b/variants/vueapp/tests/data/query-settings-trio.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:67eb829cd74131df553937e614a55aef9d2d77218069d4798dd1fa1ff55dfdd9
-size 4112
+oid sha256:1858073a2c00180b54c7f109e4cdc511f862381ec754c7534dcc0269c5480465
+size 4139
diff --git a/variants/vueapp/tests/data/retrieveFlagsEtcPresetsResponse.json b/variants/vueapp/tests/data/retrieveFlagsEtcPresetsResponse.json
index dacc2331e..47233693e 100644
--- a/variants/vueapp/tests/data/retrieveFlagsEtcPresetsResponse.json
+++ b/variants/vueapp/tests/data/retrieveFlagsEtcPresetsResponse.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:52cff730699e1763a280d16b089392721b31a1dce94b15222e83d7a2a606ba96
-size 1464
+oid sha256:5ef58b0c61994dabf8d6274b3af136a62686acb98131c8310a9fc1fd88c95ad3
+size 1491
diff --git a/variants/vueapp/tests/data/retrievePresetSetResponse.json b/variants/vueapp/tests/data/retrievePresetSetResponse.json
index 27793754a..1e1772f2a 100644
--- a/variants/vueapp/tests/data/retrievePresetSetResponse.json
+++ b/variants/vueapp/tests/data/retrievePresetSetResponse.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:e151c8e252cd27c62ecc12037744a1e356d1c90ee3ca5c26e6271f16227eaee8
-size 5451
+oid sha256:e1ea5d0775219bc19758131371fe462cfc9b8b4a83c21b5473937e2ba1ace7a3
+size 5482
diff --git a/variants/vueapp/tests/data/var-brca1-missense-benign-smallvar.json b/variants/vueapp/tests/data/var-brca1-missense-benign-smallvar.json
index 681c9b3a6..7802268c1 100644
--- a/variants/vueapp/tests/data/var-brca1-missense-benign-smallvar.json
+++ b/variants/vueapp/tests/data/var-brca1-missense-benign-smallvar.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:603f59aff7b9b4acd1d3f7a1102fc2c9d22f463158594233c7c5834e9bebf47b
-size 3206
+oid sha256:9ee65f1afde900586cf2f73d702a4737c87959738f9e8b76a6a4bd6d0aade152
+size 3233
diff --git a/variants/vueapp/tests/data/var-mtdna-noncoding-smallvar.json b/variants/vueapp/tests/data/var-mtdna-noncoding-smallvar.json
index 681c9b3a6..7802268c1 100644
--- a/variants/vueapp/tests/data/var-mtdna-noncoding-smallvar.json
+++ b/variants/vueapp/tests/data/var-mtdna-noncoding-smallvar.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:603f59aff7b9b4acd1d3f7a1102fc2c9d22f463158594233c7c5834e9bebf47b
-size 3206
+oid sha256:9ee65f1afde900586cf2f73d702a4737c87959738f9e8b76a6a4bd6d0aade152
+size 3233
diff --git a/variants/vueapp/tests/data/variants-trio.json b/variants/vueapp/tests/data/variants-trio.json
index fd8ae8b1e..ec9068ac2 100644
--- a/variants/vueapp/tests/data/variants-trio.json
+++ b/variants/vueapp/tests/data/variants-trio.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:bb047d2a9e3a05bbd569e13818c29aa37052bae394e9909dc3208e67f4801888
-size 19955
+oid sha256:7f8d616bf0dcf38bbc6d0a9ec22a059c9c36f7bcfe0556e02cbe90fd087fe029
+size 20043
diff --git a/variants/vueapp/tests/unit/components/FilterForm/FlagsPane.spec.js b/variants/vueapp/tests/unit/components/FilterForm/FlagsPane.spec.js
index b92a2b8ee..d4727f55b 100644
--- a/variants/vueapp/tests/unit/components/FilterForm/FlagsPane.spec.js
+++ b/variants/vueapp/tests/unit/components/FilterForm/FlagsPane.spec.js
@@ -24,11 +24,14 @@ describe('FilterFormFlagsPane.vue', () => {
       },
     })
 
-    expect(wrapper.findAll('input').length).toBe(28)
+    expect(wrapper.findAll('input').length).toBe(29)
 
     const effectFlagsFlagBookmarked = wrapper.get(
       '#effect-flags-flag_bookmarked',
     )
+    const effectFlagsFlagIncidentasl = wrapper.get(
+      '#effect-flags-flag_incidental',
+    )
     const effectFlagsFlagCandidate = wrapper.get('#effect-flags-flag_candidate')
     const effectFlagsFlagFinalCausative = wrapper.get(
       '#effect-flags-flag_final_causative',
@@ -115,6 +118,7 @@ describe('FilterFormFlagsPane.vue', () => {
     )
 
     await effectFlagsFlagBookmarked.setValue()
+    await effectFlagsFlagIncidentasl.setValue(false)
     await effectFlagsFlagCandidate.setValue(false)
     await effectFlagsFlagFinalCausative.setValue()
     await effectFlagsFlagForValidation.setValue(false)
@@ -149,6 +153,7 @@ describe('FilterFormFlagsPane.vue', () => {
     await effectFlagsFlagSummaryEmpty.setValue(false)
 
     expect(effectFlagsFlagBookmarked.element.checked).toBeTruthy()
+    expect(effectFlagsFlagIncidentasl.element.checked).toBeFalsy()
     expect(effectFlagsFlagCandidate.element.checked).toBeFalsy()
     expect(effectFlagsFlagFinalCausative.element.checked).toBeTruthy()
     expect(effectFlagsFlagForValidation.element.checked).toBeFalsy()